Structure of PDB 4rcv Chain A Binding Site BS02

Receptor Information
>4rcv Chain A (length=370) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLRVVVLGSTGSIGTQALQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQT
GVTNIAVADEHAAQRVGDIPYHGSDAATRLVEQTEADVVLNALVGALGLR
PTLAALKTGARLALANKESLVAGGSLVLRAARPGQIVPVDSEHSALAQCL
RGGTPDEVAKLVLTASGGPFRGWSAADLEHVTPEQAGPMNTLNSASLVNK
GLEVIETHLLFGIPYDRIDVVVHPQSIIHSMVTFIDGSTIAQASPPDMKL
PISLALGWPRRVSGAAAACDFHTASSWEFEPLDTDVFPAVELARQAGVAG
GCMTAVYNAANEEAAAAFLAGRIGFPAIVGIIADVLHAADQWAVEPATVD
DVLDAQRWARERAQRAVSGM
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain4rcv Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4rcv The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces.
Resolution2.294 Å
Binding residue
(original residue number in PDB)		G19 T21 G22 S23 I24 A46 G47 G48 A49 H50 A69 A103 L104 L108 A126 N127 E129 N209 M267
Binding residue
(residue number reindexed from 1)		G8 T10 G11 S12 I13 A35 G36 G37 A38 H39 A58 A92 L93 L97 A115 N116 E118 N190 M248
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.267: 1-deoxy-D-xylulose-5-phosphate reductoisomerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016491 oxidoreductase activity
GO:0030145 manganese ion binding
GO:0030604 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
GO:0046872 metal ion binding
GO:0050897 cobalt ion binding
GO:0070402 NADPH binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
GO:0051483 terpenoid biosynthetic process, mevalonate-independent
GO:0051484 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4rcv, PDBe:4rcv, PDBj:4rcv
PDBsum4rcv
PubMed25642788
UniProtP9WNS1|DXR_MYCTU 1-deoxy-D-xylulose 5-phosphate reductoisomerase (Gene Name=dxr)

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